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FMT and SDD show efficacy for CRE decolonisation in meta-analysis of 872 participantsCan gut bacteria transplants help clear dangerous drug-resistant infections?

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Key Takeaway
Consider FMT and SDD for CRE decolonisation but note limited evidence and potential resistance risks.

This systematic review and meta-analysis examined the efficacy and safety of decolonisation protocols for carbapenem-resistant Enterobacterales (CRE) and vancomycin-resistant enterococci (VRE) across 16 studies involving 872 participants. The interventions studied were faecal microbiota transplantation (FMT) and selective digestive decontamination (SDD), compared against various control groups. The primary outcome was clearance of CRE and VRE, with follow-up at approximately 1 month.

For FMT, clearance of CRE was significantly improved with a risk ratio (RR) of 2.01 (95% CI: 1.27-3.18). Clearance of VRE with FMT was also significantly improved with an RR of 2.96 (95% CI: 1.60-5.47). For SDD, clearance of CRE was significantly increased with an RR of 2.47 (95% CI: 1.32-4.63), while clearance of VRE with SDD was not significant (RR: 1.52, 95% CI: 0.70-3.30). Absolute numbers for these outcomes were not reported.

Adverse events with these interventions were generally mild, though serious adverse events, discontinuation rates, and tolerability details were not reported. The analysis noted low to moderate heterogeneity across studies. Several studies reported that SDD was associated with increased antimicrobial resistance, and the durability of SDD effects appears limited. Key limitations include the observational nature of most included studies, which precludes definitive causal conclusions, and the short follow-up period of approximately 1 month.

These findings suggest that both FMT and SDD may offer approaches to decolonisation of multidrug-resistant organisms, particularly for CRE. However, clinicians should interpret these results cautiously given the evidence heterogeneity, potential for antimicrobial resistance development with SDD, and need for longer-term efficacy and safety data. The analysis supports further investigation in controlled trials.

Imagine carrying bacteria in your gut that most antibiotics can't touch. These 'superbugs' — CRE and VRE — can cause devastating infections and spread to others. For people who carry them without symptoms, clearing them from the gut is a major challenge. A new analysis looked at whether two approaches could help: transplanting healthy donor stool (FMT) or using a targeted antibiotic rinse (SDD).

The review pooled data from 872 people across 16 studies. It found that stool transplants significantly improved the clearance of both CRE and VRE. The targeted antibiotic rinse also helped clear CRE, but its effect on VRE wasn't clear. This means there are tools that can shift the gut's bacterial community away from these dangerous residents.

However, the story isn't simple. The antibiotic rinse approach was linked to increased antibiotic resistance in several of the studies, which is a serious concern. The effects also appear to be temporary. We don't have clear data on serious side effects or how long the benefits last. The evidence comes from combining many smaller studies, which adds some uncertainty.

This analysis shows that manipulating the gut microbiome is a real pathway for tackling these superbugs. But it's early. The trade-offs, especially with antibiotics, and the durability of the effect are key questions that need answering before this becomes routine care.

What this means for you:
Gut bacteria transplants show promise for clearing drug-resistant superbugs, but effects may be temporary.

Study Details

Study typeMeta analysis
Sample sizen = 872
EvidenceLevel 1
Follow-up1.0 mo
PublishedApr 2026
View Original Abstract ↓
BACKGROUND: Rises in the prevalence of multi-drug-resistant organisms threaten patient safety globally. Vancomycin-resistant enterococci (VREs) and carbapenem-resistant Enterobacterales (CRE) are linked with prolonged hospitalisation, treatment failure, and increased mortality. Decolonisation strategies could reduce transmission and improve outcomes, but their efficacy and safety remain uncertain. This study systematically evaluates decolonisation protocols for VRE and CRE through a meta-analysis. METHODS: Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic review and meta-analysis were performed on studies using PubMed, ScienceDirect, Web of Science, and Scopus. Studies evaluating decolonisation protocols for VRE and CRE were included. Papers were assessed for risk of bias using the Risk of Bias 2 tool and Newcastle-Ottawa Scale. Meta-analyses were performed using RevMan, Cochrane, London, United Kingdom. RESULTS: Sixteen studies with a total of 872 participants were included for meta-analysis. Faecal microbiota transplantation (FMT) significantly improved clearance of CRE (risk ratio [RR]: 2.01; 95% confidence interval [CI]: 1.27-3.18) and VRE (RR: 2.96, 95% CI: 1.60-5.47) compared with controls, with low to moderate heterogeneity. Selective digestive decontamination (SDD) significantly increased clearance of CRE (RR: 2.47, 95% CI: 1.32-4.63), but not VRE (RR: 1.52, 95% CI: 0.70-3.30). Adverse events were generally mild, but SDD was associated with increased antimicrobial resistance in several studies. CONCLUSIONS: FMT and SDD are promising interventions for CRE decolonisation, with FMT also showing benefit in VRE. The durability of SDD effects appears limited, with significant risk of promoting resistance. Future studies should standardise endpoints, evaluate combination approaches, and explore bacteriophage therapy. We suggest implementing uniform terminology with 'provisional clearance' as a descriptor for eradication at 1 month post intervention and 'enduring clearance' following continuous eradication for 6 months.
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